SMTL ID : 6w89.1 (1 other biounit)

Structure of DNMT3A (R882H) in complex with CGA DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 5 residues within 4Å: Chain A: R.176, L.178, A.179, R.272, H.273 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.176, A:A.179, A:H.273 Water bridges: A:T.181, A:H.273 Salt bridges: A:R.176, A:R.272, A:H.273, A:H.273 CIT.3: 5 residues within 4Å: Chain C: R.176, A.179, T.181, R.272, H.273 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.273 Hydrogen bonds: C:A.179 Salt bridges: C:R.176, C:R.272

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 17 residues within 4Å: Chain A: F.13, D.14, G.15, I.16, T.18, S.36, E.37, V.38, C.39, D.59, V.60, G.80, P.82, L.103, R.264, S.265, W.266 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.16, A:T.18, A:V.38, A:D.59, A:V.60, A:R.264, A:W.266 Water bridges: A:S.42, A:R.264 pi-Stacking: A:F.13 SAH.4: 18 residues within 4Å: Chain C: F.13, D.14, G.15, I.16, T.18, S.36, E.37, V.38, C.39, D.59, V.60, R.61, G.80, P.82, L.103, R.264, S.265, W.266 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:F.13, C:G.15, C:I.16, C:T.18, C:V.38, C:C.39, C:D.59, C:V.60, C:R.61, C:R.264, C:W.266 pi-Stacking: C:F.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anteneh, H. et al., Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation. Nat Commun (2020)

Release Date

2020-04-15

Peptides

DNA (cytosine-5)-methyltransferase 3A: AC
DNA (cytosine-5)-methyltransferase 3-like: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
C

DNA (cytosine-5)-methyltransferase 3A

DNA (cytosine-5)-methyltransferase 3-like

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